oncoPredict

(Predict Response from Expression Data and Identify Cell line/Clinical Targets and Trends)

Additional details about this package can be found in our publication oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data

An R package for drug response prediction and drug-gene association prediction. The prepared GDSC and CTRP matrices for the calcPhenotype() are located in the oncoPredict OSF. * For drug response prediction, use calcPhenotype. * For pre-clinical biomarker discovery, use GLDS. * For clinical biomarker discovery, use IDWAS (for CNV or somatic mutation association with drug response) or indicate cc=TRUE (for gene expression association with drug response) in calcPhenotype(). * The link to updated CCLE gene expression data is found at depmap. We provide GDSC1/GDSC2 pre-processed expression and response data, as well as CTRP response data and depmap’s CCLE expression data (18Q2) here.

User Notes:

• Reminder that it is best to logtransform the training and test datasets (i.e. log(TPM + 1)) before batch correction (“eb”). That is, use log-transformed expression data when using calcPhenotype. ## R

• This directory contains all the R functions included in this package.

• This directory contains vignettes which display detailed examples of the functionalities available in this package.
• IDWAS This directory contains examples of IDWAS code application for clinical drug-gene association prediction.
  • cnv.Rmd Example as to how to download CNV (copy number variation) data from the GDC database, then apply map_cnv() and idwas().
  • mut.Rmd Example as to how to download stomatic mutation data from the GDC database, then apply idwas().
• GLDS This directory contains examples of GLDS code application for pre-clinical drug-gene association prediction.
  • glds_GDSC.Rmd Example of GLDS application to GDSC data.
• calcPhenotype.Rmd Example of calcPhenotype() application.

## man

• This directory contains .Rd (R documentation) files for each function. These files were automatically generated upon creation of the package.

## NAMESPACE

• This file lists the functions to be imported and exported from this package.

## DESCRIPTION

• This file contains the description documentation and metadata for this package.
• Dependencies and packages recommended for oncoPredict are listed here.

Figure 1.

Flowchart displaying the 3 primary functionalities available through oncoPredict (calcPhenotype, GLDS, IDWAS) as well as the files generated from each function and parameters. Functions and files generated are bold.